Nucleic acids and methods for the discrimination between syncytium inducing and non syncytium inducing variants of the human immunodeficiency virus

Abstract

This invention is in the area of molecular biology/virology and presents oligonucleotides with nucleotide-sequences specific for SI HIV-1 strains. These oligonucleotides may be used for in vitro determination of biological phenotype of HIV-1 strain in biological material from HIV-infected individuals by a number of techniques such as Southern and Northern blot analysis, PCR, NASBA, in situ hybridization, branched DNA hybridization, heteroduplex tracing hybridization and liquid hybridizations. HIV-1 phenotyping may i.e. be used as a diagnostic marker for disease progression or for testing efficacy of antiviral therapy.

What is claimed is:  
     
       1. An isolated and purified oligonucleotide primer having a length of 11 to 20 nucleotides, which is capable of detecting human immunodeficiency virus type 1 (HIV-1) syncytium-inducing (SI) or non-syncytium inducing (NSI) variants and comprising a nucleotide sequence at its 3′ end selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3 and SEQ ID NO:4. 
     
     
       2. The oligonucleotide primer of  claim 1 , wherein the primer is selected from the group consisting of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO.7 and SEQ ID NO:8. 
     
     
       3. A method for discriminating between syncytium inducing (SI) or non-syncytium inducing (NSI) human immunodeficiency virus type 1 (HIV-1) isolates by detecting genotypic differences at the triplet codon for amino acid position 320 of the V3 loop of the envelope glycoprotein gp120 comprising the following: 
       (a) obtaining and preparing a sample comprising viral genomic RNA, the non-coding or coding strand of viral cDNA, or the coding or non-coding strand of a proviral genome;  
       (b) performing an amplification reaction on said sample with a first primer derived from a conserved region located upstream of the V3 loop and one or more second primers containing a nucleotide sequence at the 3′ end thereof selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:2; and  
       (c) determining whether an amplification product was obtained in step (b),  
       wherein the presence of amplified product indicates the presence of an HIV-1 SI variant. 
     
     
       4. The method of  claim 3 , wherein said first primer has the sequence of SEQ ID NO:19. 
     
     
       5. The method of  claim 3 , wherein the amplification step (b) includes two of said second primers containing in one second primer a nucleotide sequence at the 3′ end thereof according to SEQ ID NO:1 and in the other second primer a nucleotide sequence at the 3′ end thereof according to SEQ ID NO:2. 
     
     
       6. A method for discriminating between syncytium inducing (SI) or non-syncytium inducing (NSI) human immunodeficiency virus type 1 (HIV-1) isolates by detecting genotypic differences at the triplet code for amino acid position 306 of the V3 loop of the envelope glycoprotein gp120 comprising the following: 
       (a) obtaining and preparing a sample comprising viral genomic RNA, the non-coding or coding strand of viral cDNA, or the coding or non-coding strand of a proviral genome;  
       (b) performing an amplification re action on said sample with one or more first primers containing a nuclotide sequence at the 3′ end thereof selected from the group consisting of SEQ ID NO:3 and SEQ ID NO:4, and a second primer derived from a conserved region located downstream of the V3 loop; and  
       (c) determining whether an amplification product was obtained in step (b),  
       wherein the presence of amplified product indicates the presence of an HIV-1 SI variant. 
     
     
       7. The method of  claim 6 , wherein said second primer has the sequence of SEQ ID NO:20. 
     
     
       8. The method of  claim 6 , wherein the amplification step (b) includes two of said first primers containing in one first primer a nucleotide sequence at the 3′ end thereof according to SEQ ID NO:3 and in the other first primer a nucleotide sequence at the 3′ end thereof according to SEQ ID NO:4.